Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0104297093:

Variant ID: vg0104297093 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4297093
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, A: 0.02, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCCCTGTTATACTACCTTGGAGTTGTATGCTTGTGTCATGCTCAAACAGCTCGACTATTCAGCCCATCCAATTTTCAAATGATCATAACGACTTATTG[T/A]
CGCAGGGTAGAGACATACAAAGAACAAAAAATAATTTTGTTTTTAAAATAGCTCAAAAGAATATTTAGTGAAATTTTATCGGGGTGAATATGTTGGGATC

Reverse complement sequence

GATCCCAACATATTCACCCCGATAAAATTTCACTAAATATTCTTTTGAGCTATTTTAAAAACAAAATTATTTTTTGTTCTTTGTATGTCTCTACCCTGCG[A/T]
CAATAAGTCGTTATGATCATTTGAAAATTGGATGGGCTGAATAGTCGAGCTGTTTGAGCATGACACAAGCATACAACTCCAAGGTAGTATAACAGGGAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.90% 42.10% 0.06% 0.00% NA
All Indica  2759 90.00% 9.90% 0.11% 0.00% NA
All Japonica  1512 12.10% 87.90% 0.00% 0.00% NA
Aus  269 8.20% 91.80% 0.00% 0.00% NA
Indica I  595 92.30% 7.70% 0.00% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 86.70% 13.00% 0.22% 0.00% NA
Indica Intermediate  786 88.70% 11.20% 0.13% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 29.60% 70.40% 0.00% 0.00% NA
Japonica Intermediate  241 4.60% 95.40% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0104297093 T -> A LOC_Os01g08630.1 downstream_gene_variant ; 774.0bp to feature; MODIFIER silent_mutation Average:34.121; most accessible tissue: Zhenshan97 flower, score: 49.964 N N N N
vg0104297093 T -> A LOC_Os01g08620-LOC_Os01g08630 intergenic_region ; MODIFIER silent_mutation Average:34.121; most accessible tissue: Zhenshan97 flower, score: 49.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104297093 9.72E-06 9.72E-06 mr1498 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0104297093 NA 2.74E-08 mr1925 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0104297093 9.64E-07 4.51E-08 mr1925 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0104297093 3.66E-07 1.56E-08 mr1498_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0104297093 NA 9.20E-08 mr1925_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0104297093 1.09E-07 1.09E-07 mr1925_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251